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  • TAU vs RPKM

    Hi all,
    i am trying to understand the difference between TAU to RPKM.

    i know that:
    The equation of Tau is :
    Ti = Vi/Li X (sigma(Vj/Lj))

    Li is the length of isoform i.
    Lj is the length of isoform j.
    Vi is the fraction of nucleotides. What does it mean?

    i also know that:
    The equation of RPKM is:
    10^9 x (Ci/(NmLi))
    Li is the length of isoform i.
    Nm is the total number of mappable reads
    Ci is the number of reads from isoform i

    i know that tau should present the relative abundance(fraction of particular transcript in the transcriptome), and RPKM is a coverage measure.

    i am trying to understand the difference by an example:

    Suppose there are only three genes (each with a single isoform), A, B, and C.
    [Scenario 1]: Suppose that the lengths of the genes are L_A = 12kb, L_B = 4kb, and L_C = 4kb.
    [Scenario 2]: Suppose that the lengths of the genes are instead L_A = 4kb, L_B =4kb, and L_C = 12kb.

    what should be the RPKM & TAU in those scenarios?

    Thanks in advance..
    Pap

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